Enhancing dependability through flexible adaptation to changing requirements

This paper describes an architectural approach that facilitates the dynamic adaptation of systems to changing domain rules. The approach relies on 'coordination contracts', a modelling and implementation primitive we have developed for run-time reconfiguration. Our framework includes an engine that, whenever a service is called, checks the domain rules that are applicable and configures the response of the service before proceeding with the call. This approach enhances dependability in two essential ways: on the one hand, it guarantees that system execution is always consistent with the domain logic because service response is configured automatically (i.e., without any need for programmer intervention); on the other hand, it makes it possible for changes to be incorporated into existing domain rules, and from new rules to be created, with little effort, because coordination contracts can be superposed dynamically without having to change neither the client nor the service code. Our approach is illustrated through a case study in financial systems, an area in which dependability arises mainly in the guise of business concerns like adherence to agreed policies and conditions negotiated on a case-by-case basis. We report on an information system that ATX Software developed for a company specialised in recovering bad credit. We show in particular how, by using this framework, we have devised a way of generating rule-dependent SQL code for batch-oriented services

DAS Writeback: A Collaborative Annotation System

<p>Abstract</p> <p>Background</p> <p>Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations.</p> <p>Results</p> <p>We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task.</p> <p>Conclusions</p> <p>We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.</p

DAS Writeback: A Collaborative Annotation System

<p>Abstract</p> <p>Background</p> <p>Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations.</p> <p>Results</p> <p>We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task.</p> <p>Conclusions</p> <p>We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.</p

Incorporating a polygenic risk score-triaged coronary calcium score into cardiovascular disease examinations to identify subclinical coronary artery disease (ESCALATE): Protocol for a prospective, nonrandomized implementation trial

Background: Identifying and targeting established modifiable risk factors has been a successful strategy for reducing the burden of coronary artery disease (CAD) at the population-level. However, up to 1-in-4 patients who present with ST elevation myocardial infarction do so in the absence of such risk factors. Polygenic risk scores (PRS) have demonstrated an ability to improve risk prediction models independent of traditional risk factors and self-reported family history, but a pathway for implementation has yet to be clearly identified. The aim of this study is to examine the utility of a CAD PRS to identify individuals with subclinical CAD via a novel clinical pathway, triaging low or intermediate absolute risk individuals for noninvasive coronary imaging, and examining the impact on shared treatment decisions and participant experience. Trial Design: The ESCALATE study is a 12-month, prospective, multicenter implementation study incorporating PRS into otherwise standard primary care CVD risk assessments, to identify patients at increased lifetime CAD risk for noninvasive coronary imaging. One-thousand eligible participants aged 45 to 65 years old will enter the study, which applies PRS to those considered low or moderate 5-year absolute CVD risk and triages those with CAD PRS ≥80% for a coronary calcium scan. The primary outcome will be the identification of subclinical CAD, defined as a coronary artery calcium score (CACS) >0 Agatston units (AU). Multiple secondary outcomes will be assessed, including baseline CACS ≥100 AU or ≥75th age-/sexmatched percentile, the use and intensity of lipid- and blood pressure-lowering therapeutics, cholesterol and blood pressure levels, and health-related quality of life (HRQOL). Conclusion: This novel trial will generate evidence on the ability of a PRS-triaged CACS to identify subclinical CAD, as well as subsequent differences in traditional risk factor medical management, pharmacotherapy utilization, and participant experience.Michael P. Gray, Yemima Berman, Giordano Bottà, Stuart M. Grieve, Amy Ho, Jessica Hu, Karice Hyun, Jodie Ingles, Garry Jennings, Gary Kilov, Jean-Frederic Levesque, Peter Meikle, Julie Redfern, Tim Usherwood, Stephen T. Vernon, Stephen J. Nicholls, and Gemma A. Figtree, On behalf of the PPP-CAD Collaborator

Philosophical determinants of obesity as a disease

Is obesity a disease? Much ink has been spilled over this debate and for good reasons. The global prevalence of obesity has more than doubled since the 1980s and is now of pandemic proportions. Whether obesity is a disease has consequences for what kind of treatments are appropriate, as well as how we ought to allocate funding and access to healthcare resources. In most cases, there is no dispute over the medical facts, yet disagreement persists. This is because whether obesity is a disease is not determined by medical facts alone; the issue is, in part, conceptual. Science relies on careful argumentation and conceptual analysis as part of its armamentarium. In this review, we will examine the two concepts of disease most often employed in the philosophy of medicine: the naturalistic and constructivist. We will argue that, whichever definition of a disease is used, obesity fits the criteria for disease definition. Those seeking to meet the challenge of managing obesity will, therefore, need to embrace chronic disease models of care suited to addressing the lifelong challenge posed by this disease and its associated complications